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bcftools merge (version 1.15.1+galaxy3)
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bcftools merge

Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file.

Note that only records from different files can be merged, never from the same file. For "vertical" merge take a look at "bcftools norm" instead.

Region Selections

Regions can be specified in a VCF, BED, or tab-delimited file (the default). The columns of the tab-delimited file are: CHROM, POS, and, optionally, POS_TO, where positions are 1-based and inclusive. Uncompressed files are stored in memory, while bgzip-compressed and tabix-indexed region files are streamed. Note that sequence names must match exactly, "chr20" is not the same as "20". Also note that chromosome ordering in FILE will be respected, the VCF will be processed in the order in which chromosomes first appear in FILE. However, within chromosomes, the VCF will always be processed in ascending genomic coordinate order no matter what order they appear in FILE. Note that overlapping regions in FILE can result in duplicated out of order positions in the output. This option requires indexed VCF/BCF files.

http://samtools.github.io/bcftools/bcftools.html#merge

https://github.com/samtools/bcftools/wiki